The work proposed here will integrate divergence population genomics and high-resolution genetics to dissect the historical and functional aspects of complex speciation between Drosophila mauritiana and its sister species, D. simulans. Since splitting ~250,000 years ago the two species have evolved complete hybrid male sterility in both directions of the cross and yet show clear evidence for recent secondary contact with gene flow (hybrid females are fertile). The goal of this project is to obtain a comprehensive genome-wide analysis of natural selection and gene flow between these partially reproductively isolated species that is informed by a fine-scale genome-wide map of hybrid incompatibility factors. The project anticipates a massive dataset currently in development: high-coverage whole-genome next-generation resequence data from 10 lines of Drosophila mauritiana and 20 lines of D. simulans. The project has two complementary components. First, novel computational and statistical inference methods will be developed for whole-genome evolutionary analysis of species divergence. Second, newly developed functional genetic resources will be used to construct a high-resolution genome-wide map of D. simulans genetic factors that cause hybrid incompatibilities in an otherwise D. mauritiana genomic background; 2-4 of these factors will be targeted for molecular identification and functional characterization. The two components will be integrated to: (1) test if incompatible regions of the genome are enriched for signatures of positive selection and/or show reduced propensity for interspecific gene flow; and (2) determine why, and the physical genomic extent to which, the X chromosome plays a seemingly special role in animal speciation.